19 papers · ranked by Valyu relevance
Safoora Masoumi, Saeid Shahraz
Background Meta-analysis is a central method for quality evidence generation. In particular, meta-analysis is gaining speedy momentum in the growing world of quantitative information. There are several software applications to process and output expected results. Open-source software applications generating such…
Károly Bósa, Paul Heinzlreiter
Background Data preparation is a fundamental aspect of data engineering, a prerequisite for later tasks such as data visualization, reporting, and training machine learning models. Despite the recurring patterns in data transformation processes, the specific steps often vary depending on the project context, data…
Tristan Deleu, Tobias Würfl, Mandana Samiei, Joseph Cohen + 1 more
'Yoshua Bengio'] The constant introduction of standardized benchmarks in the literature has helped accelerating the recent advances in meta-learning research. They offer a way to get a fair comparison between different algorithms, and the wide range of datasets available allows full control over the complexity of this…
Jingyao Wang, Chuyuan Zhang, Ye Ding, Yuxuan Yang
—Artificial intelligence technology has already had a profound impact in various fields such as economy, industry, and education, but still limited. Meta-learning, also known as "learning to learn", provides an opportunity for general artificial intelligence, which can break through the current AI bottleneck. However…
Christopher Noune, Caroline Hauxwell
A pipeline developed to establish sequence identity and estimate abundance of non-model organisms (such as viral quasispecies) using customized ultra-deep sequence ‘meta-barcodes’ has been modified to improve performance by re-development in the Python programming language. Redundant packages were removed and new…
Peter C Marks, Marc Bigler, Eric B Alsop, Adrien Vigneron + 4 more
'Bart P Lomans' 'Renato De Paula' 'Brett Geissler' 'Nicolas Tsesmetzis'] Title: Abstract The ever-increasing metagenomic data necessitate appropriate cataloguing in a way that facilitates the comparison and better contextualization of the underlying investigations. To this extent, information associated with the…
Serena Cofano, Giacomo Benedetti, Matteo Dell’Amico
Our analysis highlights issues related to dependency versions, metadata files, remote dependencies, and optional dependencies. Additionally, we identified a systematic issue with the lack of standards for metadata in the PyPI ecosystem. This includes inconsistencies in the presence of metadata files as well as…
Brandon T. Willard
In this article, we give a brief overview of the current state and future potential of symbolic computation within the Python statistical modeling and machine learning community. We detail the use of miniKanren (Byrd 2009) as an underlying framework for term rewriting and symbolic mathematics, as well as its ability to…
Joshua M. Mitchell, Yuanye Chi, Maheshwor Thapa, Zhiqiang Pang + 2 more
To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a…
Johnny Hay, Eilidh Troup, Ivan Clark, Julian Pietsch + 2 more
'Tomasz Zieliński' 'Andrew Millar'] Tools and software that automate repetitive tasks, such as metadata extraction and deposition to data repositories, are essential for researchers to share Open Data, routinely. For research that generates microscopy image data, OMERO is an ideal platform for storage, annotation and…
Mohammed Zniber, Youssef Fatihi, Tan-Phat Huynh, Sofia Forslund
Metabolomics is an emerging field within systems biology and represents the final step in the ‘omics’ cascade (, ). As a technology-driven discipline, metabolomics utilizes advancements in analytical chemistry and computational techniques to improve data collection, analysis, and interpretation (). Key platforms in…
Edd Barrett, Carl Friedrich Bolz, Lukas Diekmann, Laurence Tratt
Although run-time language composition is common, it normally takes the form of a crude Foreign Function Interface (FFI). While useful, such compositions tend to be coarse-grained and slow. In this paper we introduce a novel fine-grained syntactic composition of PHP and Python which allows users to embed each language…
Nathan J. LeRoy, Oleksandr Khoroshevskyi, Aaron O’Brien, Rafał Stepień + 2 more
As biological data increases, we need additional infrastructure to share it and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on sharing metadata. Yet, sharing metadata is also important, and in some ways has a wider scope than sharing data itself. Here…
Weiyuntian Dai, Yonglin Yi, Anqi Lin, Chaozheng Zhou + 4 more
Meta-analysis is a common statistical method used to summarize multiple studies that cover the same topic. It can provide less biased results and explain heterogeneity between studies. Although there exists a variety of meta-analysis softwares, they are rarely both convenient to use and capable of comprehensive…
Fabien Campagne, William ER Digan, Manuele Simi
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast…
Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger Sutton + 2 more
Background The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug…
Bruno Farias, Rafael Menezes, Eddie B. de Lima Filho, Youcheng Sun + 1 more
'Lucas C. Cordeiro'] This paper introduces a tool for verifying Python programs, which, using type annotation and front-end processing, can harness the capabilities of a bounded model-checking (BMC) pipeline. It transforms an input program into an abstract syntax tree to infer and add type information. Then, it…
Eftychia Eva Kontou, Axel Walter, Oliver Alka, Julianus Pfeuffer + 5 more
Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for…
Robert Dyer, Jigyasa Chauhan
Python is a multi-paradigm programming language that fully supports object-oriented (OO) programming. The language allows writing code in a non-procedural imperative manner, using procedures, using classes, or in a functional style. To date, no one has studied what paradigm(s), if any, are predominant in Python code…